GapMind for catabolism of small carbon sources

 

Aligments for a candidate for hcl in Pseudomonas fluorescens FW300-N2E3

Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate AO353_25695 AO353_25695 AMP-binding protein

Query= SwissProt::Q8GQN9
         (527 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_25695 AO353_25695
           AMP-binding protein
          Length = 554

 Score =  189 bits (480), Expect = 2e-52
 Identities = 154/492 (31%), Positives = 232/492 (47%), Gaps = 20/492 (4%)

Query: 47  AGSYTYDELALRVNRCGSALRTTLGLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAIN 106
           + +YT+ +L  +  R  + L    G++  D+V   +   ++         + G V   + 
Sbjct: 55  SATYTFSDLQDKAARFANFLLAQ-GVKKGDKVAGLLPRNVELLIVVFATWRIGAVYQPLF 113

Query: 107 TLLTESDYEYMLTDSAARVAVVSQELLPLFAPMLGKVPTLEHLVVAGGA-------GEDS 159
           T       E+ L  S A V V       +  P L  V     +V  GG        G+ S
Sbjct: 114 TAFGPKAIEHRLNSSGAAVVVTDA----VNRPKLNDVADCPTIVTVGGPKGQGIVRGDFS 169

Query: 160 LAALLATGSEQFEAAPTRPDDHCFWLYSSGSTGAPKGTVHIHSDLIHTAELYARPILGIR 219
             A L   S Q E      +D    +++SG+TG P   + +    I   + Y R  + +R
Sbjct: 170 FWAELPNYSAQCEPVLLDGEDPFLLMFTSGTTG-PSKALSVPLKAIVAFQSYTRDAVDLR 228

Query: 220 EGDVVFSAAKLFFAYGLGNGLIFPLAVGATAVLMAERPTPAAVFERLRRHQPDIFYGVPT 279
             D  ++ A   +AYG+  G+  PL++G          T  +    + ++      G PT
Sbjct: 229 PEDAFWNVADPGWAYGIYFGVTGPLSMGHPITFYDGPFTLESTCRVINKYGITNLTGSPT 288

Query: 280 LYASMLANPD-CPKEGELRLRACTSAGEALPEDVGRRWQARFGVDILDGIGSTEMLHIFL 338
            Y  ++A  D   +  + +LR  +SAGE L  +V R +    GV I D  G TE L + L
Sbjct: 289 AYRLLIAGGDEFARSIKGKLRIVSSAGEPLNPEVIRWFADNLGVVIHDHYGQTE-LGMVL 347

Query: 339 SNRAG---DVHYGTSGKPVPGYRLRLIDEDGAEITTAGVAGELQISGPSSAVMYWNNPEK 395
            N  G    VH G +G   PG+R+ ++DE   E++  G  G L I    S + ++   E 
Sbjct: 348 CNHHGLEHSVHVGAAGFASPGHRIVVLDEAYNELSV-GQPGILAIDRTQSPMCWFAGYEG 406

Query: 396 TAA-TFMGEWTRSGDKYLVNDEGYYVYAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEA 454
                F+G +  SGD   +N +G   + GRSDD++  SG  V P +VESALI H AV+EA
Sbjct: 407 APTKAFVGNYYLSGDTVELNPDGSISFVGRSDDVITTSGYRVGPFDVESALIEHPAVVEA 466

Query: 455 AVVGWEDEDHLIKPKAFIVLKPGYGAGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKT 514
           AV+G  D +     KAF+VL   Y A   L  +L+ HV+  LA + YPR IEFV +LPKT
Sbjct: 467 AVIGKPDPERTELVKAFVVLSAQYRASPELAEELRQHVRKRLAAHSYPREIEFVSELPKT 526

Query: 515 ATGKIQRFKLRS 526
            +GK+QRF LR+
Sbjct: 527 PSGKLQRFILRN 538


Lambda     K      H
   0.319    0.138    0.412 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 767
Number of extensions: 37
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 527
Length of database: 554
Length adjustment: 35
Effective length of query: 492
Effective length of database: 519
Effective search space:   255348
Effective search space used:   255348
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory